I am building a character that can control weather, focusing mostly on wind, water, and lightning.

He has Immunity 10, (Electrical Effects)

I want to give him some ranks in Protection, but limited to wind and water.

To describe the character, he would have this power because of how much time he has spent inside of storms. He's learned to reflexively disperse electricity from lightning strikes and other sources of electricity. Similarly he's much more resistant to being bullied by the wind, rain, and evens waves from the ocean.

How much should Protection cost in this situation? Would it be more efficient to just buy general ranks in Protection to reflect this? I know this is subject to GM approval, but do you think my description of the character would be able to warrant ranks in protection, devoid of modifiers?

If your GM aproval, you can buy Protection (limited only for Wind and Water as a -1 point per rank), so if you have Protection 6 will cost you just 3 points, or a cost of 1 power point per 2 point per rank

“The treachery of demons is nothing compared to the betrayal of an angel.”

General rule of thumb for ranked Flaws is that every -1 represents at least a 50% decrease in utility. So if only being protected against wind and water impacts you at least half the time, but less than 75% of the time, it's -1. 75% to 87.5%, -2. One of the examples given in the 2E books is Protection (Limited to Physical Attacks) is a -1 while Protection (Limited to Bludgeoning damage) is -2.

To go in another direction, you could also go with Immunity 10: Weather Effects and be specifically immune to effects with the Weather descriptor.

If you want to stick with all Electrical Immunity, you could keep that and also add Immunities vs Wind and Water, each at Half Effect, for a total of 10p. Then any attack with those descriptors would be at half rank before rolling resistance. I personally prefer that to limited Protection, and it scales really well.

Sorry, I can't hear your argument for realism over the sound of my eye beams.